This is a full and complete write-up on my second transmission swap on my second gen legacy outback. I will try to be as detailed as possible for anybody that is thinking of attempting this to get an idea of the amount of work involved. This project requires a lot of mechanical knowledge, money, time, resources, and most importantly the ability to find a way around anything one may encounter. As this was my second time doing this, I ass-u-med that it would be easier the second time around. I was wrong. I hoped to get it back on the road within half a week or so, but it ended up taking a full week of searching for parts, ordering and waiting for parts, among many other problems. This is a very long and thorough write up, but I'd rather include too much info than not enough. So bare with me.....

This is the boring part, but is definitely worth including as a background. I got the car for cheap ($550) with a dying 2.5. I picked up a 2.2 engine for $300 and with the help of Legacygt.com (specifically 987687), discovered that the 2.2 plugs right in, with little to no modifications. I got the car back on the road within a month or so and really lucked out with the engine that I got. It was in great shape. The car had some issues that needed to be addresses, but none were urgent. Brakes, exhaust, fluid changes.... There was just one problem with the engine that I got. It did not have an EGR set up (exhaust gas recirculation). This is an emissions related "fuel saver" that threw a Check Engine Light (CEL) almost immediately. So I could not pass inspection. I tried tricking the computer but nothing seemed to work. I dealt with the issue a few months later and about 10,000 miles by finding an even cheaper engine for $150. Its easy enough to replace that I didnt feel like replacing the whole manifold and welding into the headers to get true exhaust gas. I later found out from 987687 on LGT.com that instead of welding into the exhaust, one can reroute to the intake past the MAF before the throttle body. Huge thanks go to the infinite help I have received from him. Anyway, this cheaper engine was not in as good shape as the first one I got. But it still ran fine so I kept it for another 7,000 miles or so. It turns out that the manual 2.2s did not come with EGR, but the automatics did. All of the 2nd gen 2.5 outbacks came with EGR I believe. At one point I tried a manual 2.5 OB ECU but it did not work, prior to finding out that it was only the 2.2 MTs that came without it. I thought that if I change the car to a manual, and the computer thinks it has a manual, then I theoretically could use an engine without EGR and it would not throw a code. After the swap I discovered that it still threw an EGR code, and later found out that only the 2.2 MTs had no EGR. So I will need to find a brain thats from a 98 2.2, and in theory I should no longer get an EGR code. *fingers crossed*

So one day the car starts acting up. I still think it is possessed because I still haven't found the problem. It idled high, around 1,000 or 1,100 RPM. While I was driving, the car would go into fail-safe mode. This retards the timing and gives the engine very little power, and doesn't let it rev past 4500 rpm in hopes to save the engine from internal damage because it thinks something is horribly wrong. The code it threw initially was P1507: Idle Air Control Valve (IACV) malfunction fail-safe. This made sense because it seemed to only happen while I came to a stop in D, when the revs would fall to idle. A high idle can also clog up an IACV. It did not happen all the time but it was too frequent. If I turned the car off and back on it would reset itself, but would usually just happen again the next time I stopped. So I had a third 2.2 that I got for $60 and mainly used for parts. I swapped over the IACV but it did the same exact thing immediately. So that probably wasn't the cause of it. I tinkered with the throttle cable to make sure that the TB wasn't open just a little too far. That did not help. I replaced the TPS (throttle position sensor) from one I grabbed at the junkyard. That did not help. It seemed that everything I tried was not working. The AT OIL TEMP light occasionally flashed 16x upon start up after going into limp mode. The owners manual says "there is a problem with the trans control. see dealer." As if............. I tried the secret handshake I got from ultimatesubaru, but could not seem to get it to work, as was the case with most of the posts on that thread.

My thoughts were, maybe the trans was putting the engine into limp mode to save the trans from damage. The 4EAT always shifted funny from the first day I drove it. It shifted hard from 1st to 2nd, and hesitated, sometimes 3 seconds or more, from 2nd to 3rd. I read that if you change the fluid a bunch of times it will cure it, but after the 3rd fluid change I just gave up. It never seemed to get any worse in the 17,000 miles that I drove it. I thought maybe the trans realized it was failing and was trying to do something about it (typical limp mode for an AT is to stay in 3rd, but it still shifted through all the gears). This was a good chance to get rid of the 4EAT while I had a chance. The rest of the car is in good shape and wanted to hang onto it. And if it was an engine issue, I could use the old 2.2 (the original replacement without EGR) to hopefully solve the issue.

The car that was swapped was a 1998 Legacy Outback Limited, 30th anniversary ed, (yes with dual sunroofs!!). I live in central NH but ended up doing the swap in PA with a warm garage and my brother and friends to help. I packed up everything that I could think of that I might need in the back of the wagon and hauled it down the 370 miles to PA with the chance of it going into limp mode. It drove fine on the highway so long as I didnt come to a stop. It actually made it the whole way without going into limp mode once. I only stopped once for gas and a bathroom break. I brought the trans, rear diff, engine, driveshaft, trans xmember, clutch, flywheel, along with many tools, fluids, and spare bolts. She was very weighed down, I hit the bump stops more than once :D yay for wagons! The first few days I spent waiting for some more parts and trying to diagnose the problem with my buddy Spencebot.

Here's a list of the parts I needed. I thought of mostly everything before I got started, but there were many unforeseen missing linkages and brackets that I needed. Many mistakes and chances taken....

$20- Transmission crossmember with trans mount. Ran into a big problem with this....
300- 5MT tranny and rear diff combo (ratios MUST match!) from an '00 legacy GT. 4.11 final drive.
40- driveshaft (the MT is longer than the AT)
20- short shifter (did not fit, did not use)
64- shifter linkage (from an 09 impreza)
43- heater core hoses and clamps (they were deteriorating and it would have been stupid to not to do while the engine was out
5- exhaust gaskets
32- thermostat from Subaru (I've had bad luck with aftermarket ones...)
128- Clutch kit
29- pedal assembly (just need the clutch/brake. The gas pedal is the same on the AT and MT)
45- master cylinder, slave cyl and clutch lines. Failed, ended up having to buy replacements,
30- replacement master and slave
37- starter (found at junkyard, looked at the mileage on the car i took it off of after I removed it. car had 258k on it... the starter is very tired
91- 5 qts of royal purple 75W-90 gear oil for the tranny and rear diff.
16- coolant and muffler repair kit
48- linkage for shifter that did not come with the assy
55- clutch fork with clips and boot, washer and bushing for shift linkage, and flywheel bolts (the ones that hold on the flywheel are longer than the ones that hold on the flexpate on the AT)
115- bracket on the back of the trans that hold the shifter on, clutch bolts (hold the clutch to flywheel), and CV boot repair kit (both front inner boots were torn)
15- washers and bolts that should have been on the trans. a few were missing. I knew it had been taken apart but there were also important sensors that were missing, Neutral and reverse switches, along with the speed sensor.

Total I spend more than $1,100. This was a couple hundred more than I wanted to spend. There were so many odds and ends that needed to be addressed for the swap to be a success. My main problem with this project was that I did not have one specific donor car. I grabbed all the parts from many vehicles and many different sources. This was a BIG mistake. I spent way more than I needed to and ran into so many problems. Having a donor car is not necessary, but extremely encouraged. I spent so much time and money fixing or adding stuff that should have been there in the first place. While the engine was out of the car, I replaced the timing belt and water pump with spare new parts because I did not know how many miles were on the current one. After taking it apart, it appeared pretty worn. I'm glad I replaced it. As I was doing the water pump, Spencebot regreased the pulleys which were also very worn. While the trans was out, I had my brother replace the CV boots.

Here is the process as clearly as I can remember step by step. I lost track of the days as they passed but the whole process took about a week including waiting for parts and searching for solutions.....

Started off by unloading everything from the car. Used the engine hoist to take out the engine I would be using from the cargo area. Cleaned and prepped the garage for the swap. Put the car on jack stands and started taking it apart. Started with the exhaust and heat shield under the driveshaft. I drained the rear diff and the trans fluid before taking them out. I also drained the coolant and took out the radiator. I removed everything in the engine bay so that the engine and trans could come out freely. I took out the front left axle bolt and the control arm so that the axle would come out. I left the axle on the other side in like I did with my last swap. As long as you remove the pin, it will slide out with relative ease when the trans comes out. Just remember to slide it out and slide it back into place when removing/ installing the trans. I removed the tail section of the driveshaft so that I could tackle the rear differential.

The bolts on the back of the rear diff were very rusted, but I managed to get a grip on them and break them free after some struggling. Eventually I got the diff to fall, lowering it with the jack. The front end of the diff had to be lowered first, then the whole thing had to slide forwards. This is because the studs that hold it to the rear subframe sticks out pretty far and has to slide out. After the studs were free, the diff was hanging by the 2 rear axles which did not need to be removed. After some careful prying, we got both axles free and finally the rear diff was out. While the process was fresh in my head I started putting the new diff in. In reverse order, I got both axles partially in the diff, and managed to bolt it into place. The 2 axles popped out but would not pop back in all the way. They were in the diff but not entirely secure. We ended up taking off the rear wheels and axle bolts, and with the biggest hammer we could find, hit the axles out of the hubs to force them to seat into the diff. It worked with both sides and we simply put the axle bolt back on to make it gut'n'tight. Rear diff was complete!

While I was waiting for my friend to wake up, and eventually show up, I tackled the pedal assembly and the shifter. The pedals are a huge PITA. It can be done without lowering the steering column, but it makes it a lot easier if theres more wiggle room. The black plastic cover comes off, and there are 2 bolts holding the column up. Simply remove those and it fall enough to get the pedals in and out. The AT brake pedal comes out fairly easily. I kept the switch used for the brake lights and transferred it over to the manual setup. The gas pedal has to be removed before the assy can come all the way out. The TCM (trans control module) is attached to the brake assy and will come out with it. The manual assy has the clutch and brake on the same frame, and it bolts right up to the same holes. Before installing all the way I had to remove the little black plug that took the place of the master cyl. After some wrestling past a huge bundle of wires it went in. I tightened it all up and reattached the gas pedal. Bolted up the steering column and put the plastic cover back. Heres the master cyl hole and the very crowded pedal assy

The AT shifter was fairly easy. The center console has to come out to get to all of the bolts and screws but it is relatively painless. There are 6 or so screws holding it in at the top, and the 2 bolts and pin holding the linkage to the trans. After unhooking that from underneath the AT shifter was free.

After removing everything that was attached to the engine and trans, it was ready to come out as one unit. We started jacking the engine hoist and got it about 6" into the air, and the whole thing started slowly sinking. The cheap engine hoist was failing us and couldnt hold up the engine and trans. We set it back in the car and tried to diagnose the hoist. I am very thankful that Spencebot knew how to drain the fluid and troubleshoot it..... I would have been screwed at that point. After some tinkering he determines that there was definitely a leak. we drained the oil and put in some thicker stuff that we had. After hours of BSing with the thing we finally got it to the point where it was manageable. It still sank but much more slowly than it was before. It was enough to finally wrestle the mass of engine and trans out of the car! During the process of moving the mass forwards, I had to crawl underneath and remove the remaining bolts holding in the AT xmember. The floor jack was ready underneath the tail of it to assist in rolling it forwards. Spencebot ingeniously used a ratchet strap to pull the tail of the trans up so that we could clear the body while lifting it over.

The next day I took care of a bunch of little things while waiting for more parts. This time I was waiting for the flywheel bolts and the bracket that held the shifter to the trans. I patched up the holes in the exhaust from the harsh salt infested NH winters which was very time consuming. I also installed the shifter linkage inside the car. It was from an 09 impreza so the boots and rubber bits didn't quite match up, but no matter, it fit in after poking some holes and shaving off some foam.

I also took out the plugs that went in place of the subframe for the MT. The MT trans crossmember is much larger than the 4EAT. Even though the MT is smaller, it sits much farther forwards than the AT and it needs a support farther forwards that bolts into the body right near the control arm bolt. There are plastic plugs that pop out. I remembered the bolts for these holes when I took one from the junkyard, you will need them

There are also two similar but smaller plugs just behind the where the shifter comes through the body. These bolt holes are for the bushing that holds the shifter in place. I also remembered these bolts from the junkyard. I believe they are the same size the bolts that hold in the pedal assy, so using some if these not rusty bolts is a good idea.

The next thing to deal with was the starter. Because the trans came out of a newer car, there are 6 or 8 bolts holding the engine to the trans, and the starter uses 2 of those bolts to mount. The older engine I have only has 4 bolts holding the engine and trans together, so we had to make a bolt out of the second hole. Spencebot had a great idea of getting a helicoil. This is essentially in the form of a spring that acts as a thread for a bolt. The hole we had to use was rather large, so we got a tap to thread the hole, and put the helicoil in between the bolt and the threaded hole. It was very difficult to get the helicoil in the threads we made because every time we twisted it, the thing effectively decompressed and wouldn't thread in. After some fancy fingerwork, he got it to work and it was the perfect fit!

After forgetting to buy the clutch bolts (the ones that hold the clutch onto the flywheel) and waiting for them to arrive, We finally assembled the clutch and attached the engine to the 5MT. It was amazing to see how much smaller the whole assy was compared to the 4EAT.

The engine hoist was still operating enough to get the MT in the car. We slowly lowered it down while putting the floor jack underneath the tail to hold it up and roll it back into place while hooking up part of the shifter. Once the engine mounts were settled into the front subframe bolted in the trans xmember to hold up the MT. I tightened all those up and reconnected most of the things on the engine. I put the radiator back in after some struggling. It seemed that the accessories like power steering pump and AC compressor were strangely close to the radiator. Even with the radiator completely attached, the AC clutch rubbed against the fan on the radiator. There was something obviously wrong, this was way off.

I crawled underneath and saw that the shifter was wedged up against the body, forcing the entire engine and trans forwards while twisting the engine mounts. I thought maybe because the shift linkage was from an 09 impreza that maybe it was a different length. I managed to free the linkage but the engine/trans did not move back into place like i was expecting. I was baffled. I could not figure it out. It was obvious that it was not sitting right. The torsion mount (that attached from the firewall to the top of the trans was not even close to lining up.

The next day we got a fresh look at it, and we realized that the Outback not only has higher springs and shocks to make it taller than the legacy, but also has spacers in the subframes that are about an inch and a quarter or 3 cm that separate it from the body. This effectively lowers the center of gravity of the car by lowering the whole drivetrain on the outbacks. The trans subframe I got was from an impreza, which bolted right up. This basically pivoted the entire engine/trans on the front subframe. the tail of the trans was up too high and it was in turn making the front of the engine too far forward. We searched for the whole day trying to find longer bolts that would fit, and spacers to secure it to the body. We found some temporary washers and put it into place.

Later on, we found out that the trans xmember is shaped differently. the front has 2 thick spacers welded to it, and the arch in the back is much shorter. We grabbed one from the junkyard and this was one of the last things we replaced before got it on its wheels. This helped to resolve the shifter being too long as well. I think it is still a little too long, but it fits in and shifts great. Now everything fits the way it should. You can see by the red markings how different the subframes are when they are next to each other. The second pic you can kinda see the thick spacer they used. Sorry for the crappy pic quality

The next day I finished hooking everything up on the engine. I installed the master and slave cylinders and hooked it up to the pedals. We had to wait for yet more parts.... one of the linkages that holds the shifter linkage onto the trans, the one that actually selects the gear, was missing from both the tranny and the shifter linkage. Thankfully we got it without too long of a wait. But there was a piece missing.... We attached it but the shifter was super floppy and definitely not right. I crawled underneath and realized that one of the bolts was moving freely inside the bushing. There should have been a small cylindrical piece that slides into those two blue plastic bushings. It was so frustrating that this didnt come with it. Spencebot yet again came to the rescue and manufactured a cylinder shape by bending a section of brass into the exact shape and soldering it and sanding it smooth. It looks like it should have came with it to begin with, it fit perfectly.

The linkage that we had to order, and the brass cylinder that my friend made

Next we had to tackle the wiring. In my previous swap, the speed sensors were different on the AT and MT. But on this one, the speed sensor (VSS) just screwed out of the auto and right into the manual. No soldering or anything. We had to grab some reverse and neutral switches from the junkyard. The tranny should have come with them but didnt. We then inserted a pin into the blank slot on the ECU and grounded it to tell it that its a manual. This is pin 81, AT/MT identifier pin. We then ran a wire through a hole in the firewall that reads the neutral switch (NSS). This was pin 82 on the ECU. Open circuit means its in gear, and grounded makes it think it is in Neutral. For whatever reason its the opposite on the AT. Typically with a manual swap you need to trick the car into thinking its in P so that the key will come out. Fortunately on my car that part had broken a long time ago, so even with the auto, it let the key out in any gear. iluvdrt on legacygt.com says that you can splice the two wires from the black switch on the auto shifter and it should let the key out. I have not tried this though. As for the reverse lights, it we poked and prodded until we found the wires under the hood. Turns out to be green with yellow stripe and black with red stripe. That we connected to the reverse switch in the trans.

We finally took it for a test drive and everything seemed to be working smoothly. It was a relief to finally see the trans work. The next day we were on our way to the junkyard for some odds and ends and the clutch started sticking halfway. Eventually it just stopped working. good thing we were on our way to the junkyard! My friend came and rescued us and took us to the JY to get replacement parts

Turns out there was a huge leak......... We werent quite sure where it was coming from so while we were at the junkyard we got a master and a slave, and my buddy had a stainless steel clutch line for his 2013 BRZ. All of which fit right in and its working great now. The transmission is in GREAT shape. It feels brand new, the synchros are perfect. The thing runs like a brand new car aside from the exhaust leaks. So far I've put a little over 1,000 miles on it and its working beautifully. It made it the 400 mile back to NH and has been taking me to school. It is a great daily driver.

As for the original issue that I had with the limp mode, it still happens, but not as frequently. I can seem to control it a little better with the manual. It is still a problem though. I replaced some of the things that stayed with the swap: the MAF and the VSS, which leaves the ECU, the AF sensor, the o2 sensor, or a bad connection somewhere. I am still tinkering and will post if I ever figure out this problem...

MANY MANY THANKS go to:

my great friend Spencer for devoting so much time to helping me
my brother for helping with random odds and ends..
987687 from legacygt.com for giving me a huge amount of useful information
iluvdrt on legactgt.com for his writeup, which can be found here: http://legacygt.com/forums/showthrea...on-136840.html

So I finally discovered what was causing the occasional limp mode or "fail-safe" mode. It turns out that a few days before it started doing this, I took out the speedometer cluster to try to put in the 140mph cluster. It wasn't because it goes to 140 (the 2.2 probably won't make it there under its own power :D ), but because the needles are white and easier to see at night. Anyway, the plug that sends the speed signal to the speedo itself is a different plug than the stock (120mph) one. So I disassembled the cluster and took out the speedo gauge itself and swapped it into the stock cluster so that it would plug in. I took it for a test drive and as I expected, it read about 38mph when I was actually doing 30. So obviously that wasn't going to work. I put everything back to the way it was and made the mistake of cross threading one of the 4 tiny screws holding the speedo in, and wasn't making enough contact with the circuit board on the back of the cluster. I took out the screw and made sure it went back in straight, and made contact with the circuit board on the back. I put it all back together and checked the codes one last time before I cleared them, and it finally threw P0500, speedometer circuit, which it had never thrown before. I heard of this problem from 987687 on legacygt.com and ultimatesubaru.com. I've driven over 1,000 miles since that fix and it hasn't gone into limp mode once. problem solved!

I've put over 3,000 miles on the manual swapped drivetrain so far, and all is well! So far nothing is leaking and everything is working smoothly.

Hemingway

03-01-2013 03:19 PM

An outstanding write up ... very well done!

jshepeck

12-20-2014 06:05 PM

I have a 99 OB automatic that i did the same swap on except I used the 2.5DOHC motor. I was wondering how you got the two wire VSS wired up to the speedo through the TCM. I have all the wiring diagrams but am having a hard time trying to get it to work. Mine also goes into limp mode every key cycle and my gas gauge lies to me. Any answers or tips would be greatly appreciated.

startingtolikesubaru

07-01-2016 12:36 AM

What oil seal did you use on the outside of the differential case?
I went to subaru and they told me that the 1998 Subaru outback legacy doesn't have one and there was no part number.